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Mascardi MF, Mazzini FN, Suárez B, Ruda VM, Marciano S, Casciato P, Narvaez A, Haddad L, Anders M, Orozco F, Tamaroff AJ, Cook F, Gounarides J, Gutt S, Gadano A, García CM, Marro ML, Penas Steinhardt A, Trinks J. Integrated analysis of the transcriptome and its interaction with the metabolome in metabolic associated fatty liver disease: Gut microbiome signatures, correlation networks, and effect of PNPLA3 genotype. Proteomics 2023; 23:e2200414. [PMID: 37525333 DOI: 10.1002/pmic.202200414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
Interactions between communities of the gut microbiome and with the host could affect the onset and progression of metabolic associated fatty liver disease (MAFLD), and can be useful as new diagnostic and prognostic biomarkers. In this study, we performed a multi-omics approach to unravel gut microbiome signatures from 32 biopsy-proven patients (10 simple steatosis -SS- and 22 steatohepatitis -SH-) and 19 healthy volunteers (HV). Human and microbial transcripts were differentially identified between groups (MAFLD vs. HV/SH vs. SS), and analyzed for weighted correlation networks together with previously detected metabolites from the same set of samples. We observed that expression of Desulfobacteraceae bacterium, methanogenic archaea, Mushu phage, opportunistic pathogenic fungi Fusarium proliferatum and Candida sorbophila, protozoa Blastocystis spp. and Fonticula alba were upregulated in MAFLD and SH. Desulfobacteraceae bacterium and Mushu phage were hub species in the onset of MAFLD, whereas the activity of Fonticula alba, Faecalibacterium prausnitzii, and Mushu phage act as key regulators of the progression to SH. A combination of clinical, metabolomic, and transcriptomic parameters showed the highest predictive capacity for MAFLD and SH (AUC = 0.96). In conclusion, faecal microbiome markers from several community members contribute to the switch in signatures characteristic of MAFLD and its progression towards SH.
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Affiliation(s)
- María Florencia Mascardi
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Flavia Noelia Mazzini
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
| | - Bárbara Suárez
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Vera M Ruda
- Biotherapeutic and Analytical Technologies, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Sebastián Marciano
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Paola Casciato
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Adrián Narvaez
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Leila Haddad
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Ana Jesica Tamaroff
- Nutrition Department of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Frank Cook
- Analytical Sciences & Imaging Department, NIBR, Cambridge, Massachusetts, USA
| | - John Gounarides
- Analytical Sciences & Imaging Department, NIBR, Cambridge, Massachusetts, USA
| | - Susana Gutt
- Nutrition Department of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Adrián Gadano
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Celia Méndez García
- Chemical Biology & Therapeutics Department, NIBR, Cambridge, Massachusetts, USA
| | - Martin L Marro
- Cardiovascular and Metabolic Disease Area, NIBR, Cambridge, Massachusetts, USA
| | - Alberto Penas Steinhardt
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Laboratorio de Genómica Computacional, Universidad Nacional de Luján, Lujan, Buenos Aires, Argentina
| | - Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Aguilera P, Mascardi MF, Belforte FS, Rosso AD, Quesada S, Llovet I, Iraola G, Trinks J, Penas-Steinhardt A. A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic. Front Microbiol 2022; 13:803121. [PMID: 35401432 PMCID: PMC8988235 DOI: 10.3389/fmicb.2022.803121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 01/02/2023] Open
Abstract
The COVID-19 pandemic poses a great challenge to global public health. The extraordinary daily use of household disinfectants and cleaning products, social distancing and the loss of everyday situations that allow contact between individuals, have a direct impact on the transfer of microorganisms within the population. Together, these changes, in addition to those that occur in eating habits, can affect the composition and diversity of the gut microbiota. A two-time point analysis of the fecal microbiota of 23 Metropolitan Buenos Aires (BA) inhabitants was carried out, to compare pre-pandemic data and its variation during preventive and compulsory social isolation (PCSI) in 2020. To this end, 23 healthy subjects, who were previously studied by our group in 2016, were recruited for a second time during the COVID-19 pandemic, and stool samples were collected from each subject at each time point (n = 46). The hypervariable region V3-V4 of the 16S rRNA gene was high-throughput sequenced. We found significant differences in the estimated number of observed features (p < 0.001), Shannon entropy index (p = 0.026) and in Faith phylogenetic diversity (p < 0.001) between pre-pandemic group (PPG) vs. pandemic group (PG), being significantly lower in the PG. Although no strong change was observed in the core microbiota between the groups in this study, a significant decrease was observed during PCSI in the phylum Verrucomicrobia, which contributes to intestinal health and glucose homeostasis. Microbial community structure (beta diversity) was also compared between PPG and PG. The differences observed in the microbiota structure by unweighted UniFrac PCoA could be explained by six differential abundant genera that were absent during PCSI. Furthermore, putative functional genes prediction using PICRUSt infers a smaller predicted prevalence of genes in the intestinal tryptophan, glycine-betaine, taurine, benzoate degradation, as well as in the synthesis of vitamin B12 during PCSI. This data supports the hypothesis that the microbiome of the inhabitants of BA changed in the context of isolation during PCSI. Therefore, these results could increase the knowledge necessary to propose strategic nutraceutical, functional food, probiotics or similar interventions that contribute to improving public health in the post-pandemic era.
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Affiliation(s)
- Pablo Aguilera
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
| | - Fiorella Sabrina Belforte
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Genómica Computacional (GEC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
- Departamento de Ciencias Básicas, Instituto de Ecología y Desarrollo Sustentable (INEDES) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UNLu, Universidad Nacional de Luján, Luján, Argentina
| | - Ayelén Daiana Rosso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Genómica Computacional (GEC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
- Departamento de Ciencias Básicas, Instituto de Ecología y Desarrollo Sustentable (INEDES) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-UNLu, Universidad Nacional de Luján, Luján, Argentina
| | - Sofía Quesada
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Genómica Computacional (GEC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
| | - Ignacio Llovet
- Departamento de Ciencias Sociales, Universidad Nacional de Luján, Luján, Argentina
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Julieta Trinks
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
| | - Alberto Penas-Steinhardt
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Genómica Computacional (GEC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Argentina
- Fundación H.A. Barceló, Instituto Universitario de Ciencias de la Salud, Buenos Aires, Argentina
- *Correspondence: Alberto Penas-Steinhardt,
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Mazzini FN, Cook F, Gounarides J, Marciano S, Haddad L, Tamaroff AJ, Casciato P, Narvaez A, Mascardi MF, Anders M, Orozco F, Quiróz N, Risk M, Gutt S, Gadano A, Méndez García C, Marro ML, Penas-Steinhardt A, Trinks J. Plasma and stool metabolomics to identify microbiota derived-biomarkers of metabolic dysfunction-associated fatty liver disease: effect of PNPLA3 genotype. Metabolomics 2021; 17:58. [PMID: 34137937 DOI: 10.1007/s11306-021-01810-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Non-invasive biomarkers are needed for metabolic dysfunction-associated fatty liver disease (MAFLD), especially for patients at risk of disease progression in high-prevalence areas. The microbiota and its metabolites represent a niche for MAFLD biomarker discovery. However, studies are not reproducible as the microbiota is variable. OBJECTIVES We aimed to identify microbiota-derived metabolomic biomarkers that may contribute to the higher MAFLD prevalence and different disease severity in Latin America, where data is scarce. METHODS We compared the plasma and stool metabolomes, gene patatin-like phospholipase domain-containing 3 (PNPLA3) rs738409 single nucleotide polymorphism (SNP), diet, demographic and clinical data of 33 patients (12 simple steatosis and 21 steatohepatitis) and 19 healthy volunteers (HV). The potential predictive utility of the identified biomarkers for MAFLD diagnosis and progression was evaluated by logistic regression modelling and ROC curves. RESULTS Twenty-four (22 in plasma and 2 in stool) out of 424 metabolites differed among groups. Plasma triglyceride (TG) levels were higher among MAFLD patients, whereas plasma phosphatidylcholine (PC) and lysoPC levels were lower among HV. The PNPLA3 risk genotype was related to higher plasma levels of eicosenoic acid or fatty acid 20:1 (FA(20:1)). Body mass index and plasma levels of PCaaC24:0, FA(20:1) and TG (16:1_34:1) showed the best AUROC for MAFLD diagnosis, whereas steatosis and steatohepatitis could be discriminated with plasma levels of PCaaC24:0 and PCaeC40:1. CONCLUSION This study identified for the first time MAFLD potential non-invasive biomarkers in a Latin American population. The association of PNPLA3 genotype with FA(20:1) suggests a novel metabolic pathway influencing MAFLD pathogenesis.
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Affiliation(s)
- Flavia Noelia Mazzini
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Potosí 4240, C1199ACL, Ciudad Autónoma de Buenos Aires, Argentina
| | - Frank Cook
- Analytical Sciences & Imaging (AS&I) Department, Novartis Institutes for Biomedical Research (NIBR), Cambridge, MA, USA
| | - John Gounarides
- Analytical Sciences & Imaging (AS&I) Department, Novartis Institutes for Biomedical Research (NIBR), Cambridge, MA, USA
| | - Sebastián Marciano
- Liver Unit of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leila Haddad
- Liver Unit of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Jesica Tamaroff
- Nutrition Department of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paola Casciato
- Liver Unit of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrián Narvaez
- Liver Unit of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Mascardi
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Potosí 4240, C1199ACL, Ciudad Autónoma de Buenos Aires, Argentina
| | - Margarita Anders
- Liver Unit of Hospital Alemán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico Orozco
- Liver Unit of Hospital Alemán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolás Quiróz
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Potosí 4240, C1199ACL, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Risk
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Potosí 4240, C1199ACL, Ciudad Autónoma de Buenos Aires, Argentina
| | - Susana Gutt
- Nutrition Department of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrián Gadano
- Liver Unit of Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Martin L Marro
- Cardiovascular and Metabolic Disease Area, NIBR, Cambridge, MA, USA
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
| | - Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Potosí 4240, C1199ACL, Ciudad Autónoma de Buenos Aires, Argentina.
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